Dindel protocols

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Dindel specifications

Information


Unique identifier OMICS_00096
Name Dindel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped Illumina read data
Input format BAM
Output data Variant calls
Output format VCF
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Cornelis Albers <>

Publication for Dindel

Dindel in pipelines

 (15)
2017
PMCID: 5473639
PMID: 28112205
DOI: 10.1038/ncomms14209

[…] removed using samtools version 1.18 (ref. ). samtools was also used to call snps with the command: ‘mpileup –m 300 –i –g –d -c50 –s'. small insertions and deletions (indels) were identified using dindel version 1.01 (ref. ), by first identifying putative indels for each sample individually, and then re-running the dindel on the pooled set of samples from family a with the previously […]

2016
PMCID: 4806435
PMID: 27009152
DOI: 10.1186/s12864-016-2563-z

[…] by a custom perl script that selects candidate alleles from the bbmap-produced bam files and downsamples the reads into separate allele-specific bam files []. these are analysed using the program dindel [] to call the specific insertions/deletions. the script then outputs each allele found and its frequency within the sample. two custom r scripts are used to produce graphical representations […]

2016
PMCID: 5069154
PMID: 27642863
DOI: 10.1038/nchembio.2176

[…] strain, a best call was made based on the aligned reads for each strain, and positions where all strains supported a variant were discarded. small insertions and deletions (indels) were called using dindel. candidate indels found in one strain were explicitly tested for in all strains; indels with at least 70% of reads in the region supporting the indel and at positions with an average […]

2015
PMCID: 4556809
PMID: 26330513
DOI: 10.1128/mBio.00981-15

[…] correction required that at least 80% of the reads supported the snp or the reference. if the data did not support either base, then the position was called as an ambiguous base (“n”)., we used dindel v. 1.01 () to realign the sequencing reads (mapped and unmapped) and test whether candidate indels produced by bwa and samtools were supported by those reads. putative indel positions […]

2015
PMCID: 5389031
PMID: 25633131
DOI: 10.1038/srep08132

[…] pcc 6301 and synechococcus pcc 7942 genome data obtained from genbank (nc_006576 and nc_007604, respectively) using novoalign. samtools was used to identify snps between the two strains. dindel was used to identify indels. pindel and custom analyses were used to identify structural rearrangements. 454 genome sequencing was also performed in parallel (mogene lc, st. louis, mo) […]


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Dindel in publications

 (68)
PMCID: 5707812
PMID: 29213343
DOI: 10.1186/s13053-017-0082-9

[…] mark duplicated reads, perform local realignment around short insertions and deletions, recalibrate the base quality scores and call snvs and short indels together with samtools version 0.1.18 and dindel version 1.01 []. on average, 104.7 million reads were uniquely mapped. 80.9% of all targeted regions were covered >30 times, with a mean coverage of 89. scripts developed in-house […]

PMCID: 5549930
PMID: 28792971
DOI: 10.1371/journal.pone.0182272

[…] whole-exome sequencing (wes) data, we performed sanger sequencing for all indels called from the several calling algorithm. we compared the performance of the four algorithms (i.e. gatk, samtools, dindel, and freebayes) for indel detection from the same sample. we examined the sensitivity and ppv of gatk (90.2 and 89.5%, respectively), samtools (75.3 and 94.4%, respectively), dindel (90.1 […]

PMCID: 5474888
PMID: 28429735
DOI: 10.1038/ncomms14944

[…] duplicate reads were removed using picard tools. base recalibration, local realignment around indels and snv calling were performed using the genomeanalysistoolkit (gatk). indels were called using dindel. mutations were filtered based on mapping quality, and sequencing coverage. somatic mutations were further filtered by comparison with the matched germline reference and using common variant […]

PMCID: 5309787
PMID: 28186126
DOI: 10.1038/ncomms14262

[…] were detected using established pipelines based on varscan2 combined with rnaseq data and functional annotation of the variants based on ensembl v.70. somatic indels were detected using samtools and dindel., rna reads were aligned to hg19 using bwa and samtools. mapped reads were annotated using ensembl v70. gene expression levels were quantified in reads per kilobase of exon per million mapped […]

PMCID: 5473639
PMID: 28112205
DOI: 10.1038/ncomms14209

[…] removed using samtools version 1.18 (ref. ). samtools was also used to call snps with the command: ‘mpileup –m 300 –i –g –d -c50 –s'. small insertions and deletions (indels) were identified using dindel version 1.01 (ref. ), by first identifying putative indels for each sample individually, and then re-running the dindel on the pooled set of samples from family a with the previously […]


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Dindel institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK

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